水稻抗白葉枯病基因同義密碼子使用偏性之影響因素探討

Factors Influencing the Synonymous Codon Usage Bias in the Genes for Resistance to Bacterial Leaf Blight (Xanthomonas oryza pv. oryza) of Rice (Oryza sativa)

魏夢麗(Meng-Li Wei) ； 鍾依涵(Yi-Han Chung) ； 呂椿棠(Chun-Tang Lu) ； 呂秀英(Hsiu-Ying Lu)

《台灣農業研究》 59卷2期 (2010/06) Pp. 86-102

https://doi.org/10.6156/JTAR/2010.05902.03

摘要

同樣對白葉枯病菌產生抗性的不同Xa基因間，呈現出密碼子使用偏性的多樣性。因此，本研究進行Xa基因同義密碼子使用偏性之影響因素探討，以進而暸解形成密碼子使用的演化機制。研究材料係取自NCBI(National Center for Biotechnology Information)之GenBank資料庫下載已完全定序的Xa基因（Xa1, xa5, xa13, Xa13, Xa21, Xa26 及Xa27）及其家族之17個編碼區序列(coding domain sequence, CDS)，透過計算這些Xa基因的CDS長度及各種同義密碼子使用偏性指標，如同義密碼子相對使用度(relative synonymous codon usage, RSCU)、密碼子適應指標(codon adaption index, CAI)、有效密碼子數(effective number of codons, ENC)、同義密碼子第三位置出現G或C核苷酸之頻率(GC3)以及同義密碼子第一、二位置出現G或C核苷酸之平均頻率(GC12)，並分析其間之關係，以闡明同義密碼子使用偏性之主要影響因素。結果發現Xa基因之CDS長度及基因表達程度與同義密碼子使用偏性有極顯著關係，即Xa基因長度較短者可有較高的基因表達程度、以及較高的同義密碼子使用偏性，如xa5、xa13、Xa13及Xa27基因。Xa基因序列之GC3組成限制，也影響密碼子的使用。而GC3突變偏性又受到GC12之影響，造成Xa基因之同義密碼子使用偏性。

關鍵字

同義密碼子使用偏性 ； 基因表達程度 ； GC含量 ； 突變偏性 ； 分子演化

並列摘要

Codon usage bias varied among genes (Xa) conferring resistance of rice (Oryza sativa) to bacterial leaf blight caused by Xanthomonas oryzae pv. oryzae. This study was conducted to elucidate the evolution of synonymous codon usage by analysis of factors influencing the synonymous codon usage pattern of Xa genes. A total of 17 coding domain sequences (CDS) of the completely sequenced genes, Xa1, xa5, xa13, Xa13, Xa21, Xa26, and Xa27, were obtained through the access of the GenBank database of National Center for Biotechnology Information (NCBI) and they were used to unravel the main factors influencing codon usage bias. The length of CDS and indices of synonymous condon usage bias such as relative synonymous codon usage (RSCU), codon adaption index (CAI), effective number of codons (ENC), frequency of G or C nucleotides present at the third position of synonymous codons (GC3), and mean frequencies of G or C nucleotides present at the first and second positions of synonymous codons (GC12) were estimated to examine relationships among them. The length of CDS and level of gene expression were highly correlated to codon usage bias in Xa genes; the Xa genes with shorter CDS (xa5, xa13, Xa13, and Xa27) had higher gene expression and higher codon usage bias. The GC3 compositional constraints also affected the codon usage in Xa genes. Moreover, the GC12 had a direct effect on GC3 mutation bias, leading to further high codon usage bias in Xa genes.

並列關鍵字

Synonymous codon usage bias ； Gene expression level ； GC3 content ； Mutation bias ； Molecular evolution ； Bacterial leaf blight ； Xanthomonas oryzae